icn3d 3.30.0 → 3.30.1

package/icn3d.js

@@ -38196,6 +38196,7 @@ class AnnoDomain {
 
                     let result = ic.domain3dCls.c2b_NewSplitChain(atoms);
                     let subdomains = result.subdomains;
+                    let pos2resi = result.pos2resi;
                     //let substruct = result.substruct;
                     //let jsonStr = ic.domain3dCls.getDomainJsonForAlign(atoms);
 
@@ -38210,6 +38211,8 @@ class AnnoDomain {
 
                         data.domains[chainid].domains.push(domain);
                     }
+
+                    data.domains[chainid].pos2resi = pos2resi;
                 }
             }
 
@@ -38246,7 +38249,7 @@ class AnnoDomain {
         let html = '<div id="' + ic.pre + chnid + '_domainseq_sequence" class="icn3d-dl_sequence">';
         let html2 = html;
         let html3 = html;
-        let domainArray, proteinname;
+        let domainArray, pos2resi, proteinname;
         let pos = chnid.indexOf('_');
         let chain = chnid.substr(pos + 1);
         // MMDB symmetry chain has the form of 'A1'
@@ -38254,9 +38257,11 @@ class AnnoDomain {
             chain = chain.substr(0, chain.length - 1);
         }
 
-        if(bCalcDirect) {
+        // if(bCalcDirect) {
             proteinname = chnid;
             domainArray = (data.domains[chnid]) ? data.domains[chnid].domains : [];
+            pos2resi = data.domains[chnid].pos2resi;
+/*            
         }
         else {
             let molinfo = data.moleculeInfor;
@@ -38275,6 +38280,7 @@ class AnnoDomain {
                 domainArray = [];
             }
         }
+*/        
 
         for(let index = 0, indexl = domainArray.length; index < indexl; ++index) {
             //var fulltitle = '3D domain ' +(index+1).toString() + ' of ' + proteinname + '(PDB ID: ' + data.pdbId + ')';
@@ -38288,8 +38294,11 @@ class AnnoDomain {
             let resCnt = 0;
 
             for(let i = 0, il = subdomainArray.length; i < il; ++i) {
-                let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
-                let domainTo = Math.round(subdomainArray[i][1]) - 1;
+                // let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
+                // let domainTo = Math.round(subdomainArray[i][1]) - 1;
+                let domainFrom = Math.round(subdomainArray[i][0]); // convert 1-based to 0-based
+                let domainTo = Math.round(subdomainArray[i][1]);
+
                 if(domainFromHash.hasOwnProperty(domainFrom) || domainToHash.hasOwnProperty(domainTo)) {
                     continue; // do nothing for duplicated "from" or "to", e.g, PDBID 1ITW, 5FWI
                 }
@@ -38300,8 +38309,8 @@ class AnnoDomain {
 
                 // use the NCBI residue number, and convert to PDB residue number during selection
                 // if(ic.bNCBI || bCalcDirect) {
-                    fromArray.push(domainFrom);
-                    toArray.push(domainTo);
+                    fromArray.push(pos2resi[domainFrom]);
+                    toArray.push(pos2resi[domainTo]);
                 // }
                 // else {
                 //     fromArray.push(domainFrom + ic.baseResi[chnid]);
@@ -38310,7 +38319,9 @@ class AnnoDomain {
 
                 resCnt += domainTo - domainFrom + 1;
                 for(let j = domainFrom; j <= domainTo; ++j) {
-                    resiHash[j+1] = 1;
+                    // resiHash[j+1] = 1;
+                    let resi = pos2resi[j];
+                    resiHash[resi] = 1;
                 }
             }
 
@@ -38326,7 +38337,8 @@ class AnnoDomain {
                     for(let j = from; j <= to; ++j) {
                         // 0-based
                         let obj = {};
-                        let resi = ic.ParserUtilsCls.getResi(chnid, j);
+                        // let resi = ic.ParserUtilsCls.getResi(chnid, j);
+                        let resi = pos2resi[j];
                         obj[chnid + '_' + resi] = domainName;
                         ic.resid2domain[chnid].push(obj);
                     }
@@ -38347,7 +38359,8 @@ class AnnoDomain {
               html += ic.showSeqCls.insertGap(chnid, i, '-');
               //if(i >= domainFrom && i <= domainTo) {
               let resi = ic.ParserUtilsCls.getResi(chnid, i);
-              if(resiHash.hasOwnProperty(i+1)) {
+            //   if(resiHash.hasOwnProperty(i+1)) {
+              if(resiHash.hasOwnProperty(resi)) {
                   let cFull = ic.giSeq[chnid][i];
                   let c = cFull;
                   if(cFull.length > 1) {
@@ -39992,7 +40005,7 @@ class Domain3d {
 		// get a list of Calpha-Calpha contacts
 		///list< pair< pair< int, let >, let > >
 		let cts = this.c2b_AlphaContacts(seqLen, x0, y0, z0, dcut, resiArray);
-	
+
 		//
 		// Produce a "map" of the SSEs, i.e. vec_sse[i] = 0 means residue i + 1
 		// is in a loop, and vec_sse[i] = k means residue i + 1 belongs to SSE